Other uses

In Pokémon Crystal, HeartGold and SoulSilver, in the Ruins of Alph, the player requires a Water Stone to open the hidden room in the southwestern chamber. In Pokémon Crystal, the player simply needs to have it in their Bag. In Pokémon HeartGold and SoulSilver, they need to use it while facing the wall.

In the anime

In Once in a Mawile, a Water Stone belonging to Samantha appeared, which Brock's Lombre used to evolve into Ludicolo. This is the first time that a main character's Pokémon evolved via an Evolution stone on-screen.

In The Kindest Tentacruel, the Pokémon Fan Club Chairman told Yellow about a legend of an underwater dome at the bottom of Vermilion Harbor, housing a set of Evolution stones which, unlike normal stones, did not disappear after making a Pokémon evolve, allowing them to be used repeatedly. The cause of Red's Poliwhirl's evolution had been one of these said stones, proving the legend to be true. Yellow was later led to the dome by a wild Tentacruel, finding a Leaf Stone in it, but the Fire, Thunder, and Water Stones were missing. Later, it was revealed that Giovanni had given them to Red so he could freely evolve and devolve his Eevee.

Trivia

Through a glitch in the Generation I games, Pokémon that would normally require an Evolution stone to evolve can be evolved without it, provided that the Pokémon levels up in the battle and the player has sent out a specific Pokémon in the same battle. In the case of the Water Stone, this Pokémon is Onix.